Workflow

This workflow is for generating the plots relating to tranmission clustering for the project. The main result is the concordance and distance plots that will compare the SNP calls obtained from Nanopore data and those from the COMPASS pipeline for Illumina.

Click the nodes to obtain details about each step.

Clustering

Clusters

Confusion Matrix

Concordance

Plots

Distance

Plot

Mixed Tech

Simulations

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
File Code
 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
samplesheet:        "../../docs/samplesheet.csv"
baseline_dir:       "../baseline_variants"
pandora_dir:        "../pandora_variants"
qc_dir:             "../../data/QC"
adaptive_threshold: 100
thresholds:
  - 0
  - 2
  - 5
  - 12

nanopore_callers:
  - pandora_map
  - pandora_compare
  - bcftools

containers:
  conda: "docker://continuumio/miniconda3:4.7.12"

envs:
  dotplot:           "envs/dotplot.yaml"
  plot_concordance:  "envs/plot_concordance.yaml"
  clustering:        "envs/clustering.yaml"
  mixed_simulations: "envs/mixed_simulations.yaml"

scripts:
  dotplot:           "scripts/distance_dot_plot.py"
  plot_concordance:  "scripts/plot_concordance.py"
  clustering:        "scripts/clustering.py"
  mixed_simulations: "scripts/mixed_simulations.py"

bcftools_clustering_thresholds:
  0:  0
  2:  2
  5:  5
  12: 11

compare_clustering_thresholds:
  0:  0
  2:  1
  5:  3
  12: 7

map_clustering_thresholds:
  0: 16
  2: 18
  5: 18
  12: 27

Loading...